The power of Xmipp

Xmipp is a key software suite in the image processing workflow for cryo-electron microscopy (cryo-EM) single-particle analysis. Its modular protocols and deep integration with Scipion enable users to handle the complexity of cryo-EM data and achieve high-resolution 3D reconstructions.

This page highlights the relevance of Xmipp through three concrete examples: SARS-CoV-2 spike, ClpC1 and HER2-TZB. In all cases, Xmipp protocols played a critical role in various stages of data processing, from preprocessing and particle selection to final 3D refinement and validation.

Project: SARS-CoV-2 spike

Project Summary

• Sample: SARS-CoV-2 spike

• EMDB ID: EMD-11328, EMD-11336, EMD-11337, EMD-11341

• Final Resolution: 2.96 A˚

• Xmipp Version: 3.20.07 - Boreas

• Publication Melero R, Sorzano COS, Foster B, Vilas JL, Martínez M, Marabini R, Ramírez-Aportela E, Sanchez-Garcia R, Herreros D, Del Caño L, Losana P, Fonseca-Reyna YC, Conesa P, Wrapp D, Chacon P, McLellan JS, Tagare HD, Carazo JM. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. IUCrJ. 2020 Sep 29;7(Pt 6):1059–69. doi: 10.1107/S2052252520012725. Epub ahead of print. PMID: 33063791; PMCID: PMC7553147.

Protocols Used

• CTF Correction: - XmippProtCTFMicrographs

• Particle Handling: - XmippProtParticlePicking - XmippProtConsensusPicking - XmippProtDeepMicrographScreen (micCleaner)

• 3D Visualization and Validation: - XmippProtReconstructHighRes

• Postprocessing: - XmippProtDeepVolPostProc (EMhancer)

Project: CLP-C1 (Mycobacterium tuberculosis)

Project Summary

• Sample: ClpC1

• EMDB ID: EMD-15240, EMD-15242, EMD-15243, EMD-15241

• Final Resolution: 2.96 A˚

• Xmipp Version: 3.22.04 - Gaia

• Publication Weinhäupl K, Gragera M, Bueno-Carrasco MT, et al. Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. The Journal of Biological Chemistry. 2022 Nov;298(11):102553. DOI: 10.1016/j.jbc.2022.102553. PMID: 36208775; PMCID: PMC9661721

Protocols Used

• Particle Handling: - XmippProtParticlePicking

• Postprocessing: - XmippProtDeepVolPostProc (EMhancer)

Project: HER2-TZB

Project Summary

• Sample: [HER2-TZB ]

• EMDB ID: [To be completed]

• Final Resolution: [To be completed]

• Xmipp Version: [To be completed]

• Publication:

Protocols Used

• CTF Correction: - XmippProtCTFCorrectWiener2D

• Volume Processing and Refinement: - XmippProtAlignVolumeParticles - XmippProtReconstructFourier - XmippProtPreprocessVolumes - XmippProtFilterVolumes - XmippProtMaskVolumes - XmippProtMonoRes - XmippProtStructureMap - XmippProtSubtractProjection

• Particle Handling: - XmippProtCropResizeParticles

• 3D Visualization and Validation: - XmippProtCompareAngles - XmippProtCompareReprojections - XmippProtConsensusClasses - XmippProtCreateGallery - XmippProtCreateMask3D - XmippProtFSO

• Postprocessing: - XmippProtDeepVolPostProc (EMhancer)

• Model Integration: - XmippProtConvertPdb

Conclusion

The projects presented here demonstrate the transformative power of Xmipp in cryo-EM single-particle analysis. By offering an extensive suite of robust protocols—from early-stage CTF correction to advanced 3D reconstruction and postprocessing—Xmipp streamlines the entire workflow, enabling researchers to achieve exceptional structural resolutions and scientific insight.

In high-impact studies such as SARS-CoV-2 spike and ClpC1, Xmipp played a decisive role in achieving high resolution and validating structural models, directly contributing to key biological discoveries and impactful publications.

Using tools like Xmipp doesn’t just simplify data processing—it empowers users to extract the full potential of their data, reduce processing bottlenecks, and ensure reproducibility and scientific rigor. As the field evolves, Xmipp continues to integrate cutting-edge methods like deep learning, adaptive workflows, and hybrid modeling, reinforcing its role as a cornerstone for next-generation cryo-EM research.

In short, Xmipp is not just a tool—it’s an enabler of breakthrough science.